QC Report


general
Report generated at2022-10-07 11:38:04
TitleCTCF_OL-NEUN
DescriptionChIP-seq for CTCF_OL-NEUN
Pipeline versionv1.3.6
Pipeline typetf
Genomehg38
Alignerbowtie2
Sequencing endedness{'rep1': {'paired_end': False}, 'rep2': {'paired_end': False}, 'ctl1': {'paired_end': False}, 'ctl2': {'paired_end': False}}
Peak callerspp

Alignment quality metrics


SAMstat (raw unfiltered BAM)

rep1rep2ctl1ctl2
Total Reads40000000400000004000000040000000
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads36826200348179813930457339365661
Mapped Reads (QC-failed)0000
% Mapped Reads92.1000000000000187.098.398.4
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Marking duplicates (filtered BAM)

rep1rep2ctl1ctl2
Unpaired Reads33231658313196123382643534052913
Paired Reads0000
Unmapped Reads0000
Unpaired Duplicate Reads520260267643771272266957357
Paired Duplicate Reads0000
Paired Optical Duplicate Reads0000
% Duplicate Reads15.655621.59793.76122.8114

Filtered out (samtools view -F 1804):


SAMstat (filtered/deduped BAM)

rep1rep2ctl1ctl2
Total Reads28029056245552353255416933095556
Total Reads (QC-failed)0000
Duplicate Reads0000
Duplicate Reads (QC-failed)0000
Mapped Reads28029056245552353255416933095556
Mapped Reads (QC-failed)0000
% Mapped Reads100.0100.0100.0100.0
Paired Reads0000
Paired Reads (QC-failed)0000
Read10000
Read1 (QC-failed)0000
Read20000
Read2 (QC-failed)0000
Properly Paired Reads0000
Properly Paired Reads (QC-failed)0000
% Properly Paired Reads0.00.00.00.0
With itself0000
With itself (QC-failed)0000
Singletons0000
Singletons (QC-failed)0000
% Singleton0.00.00.00.0
Diff. Chroms0000
Diff. Chroms (QC-failed)0000

Filtered and duplicates removed


Sequence quality metrics (filtered/deduped BAM)

rep1
rep1
rep2
rep2

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.


Library complexity quality metrics


Library complexity (filtered non-mito BAM)

rep1rep2ctl1ctl2
Total Fragments33221322313054223380337934022952
Distinct Fragments28213903247839333265897733192308
Positions with Two Read370977643026781083011794111
NRF = Distinct/Total0.8492710.7916820.9661450.975586
PBC1 = OneRead/Distinct0.8472190.7860390.965930.975569
PBC2 = OneRead/TwoRead6.4433414.52767629.12831640.776883

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline


NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally


Replication quality metrics


IDR (Irreproducible Discovery Rate) plots

rep1_vs_rep2
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
pooled-pr1_vs_pooled-pr2

Reproducibility QC and peak detection statistics

overlapidr
Nt11902136447
N110355332067
N29636831566
Np12008935318
N optimal12008936447
N conservative11902136447
Optimal Setpooled-pr1_vs_pooled-pr2rep1_vs_rep2
Conservative Setrep1_vs_rep2rep1_vs_rep2
Rescue Ratio1.0089732064089531.031966702531287
Self Consistency Ratio1.07455794454590731.0158715073180005
Reproducibility Testpasspass

Reproducibility QC


Number of raw peaks

rep1rep2
Number of peaks299999299997

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics


Peak region size

rep1rep2idr_optoverlap_opt
Min size220.0235.0228.0228.0
25 percentile880.0940.0486.0910.0
50 percentile (median)880.0940.0554.0910.0
75 percentile880.0940.0910.0910.0
Max size987.01149.01291.01291.0
Mean849.3000443334811905.8889955566223615.8051965868246816.2760619207421

rep1
rep1
rep2
rep2
idr_opt
idr_opt
overlap_opt
overlap_opt

Enrichment / Signal-to-noise ratio


Strand cross-correlation measures (trimmed/filtered SE BAM)

rep1rep2
Number of Subsampled Reads1500000015000000
Estimated Fragment Length610680
Cross-correlation at Estimated Fragment Length0.1501672806157880.13809455402583
Phantom Peak105105
Cross-correlation at Phantom Peak0.18958680.2003833
Argmin of Cross-correlation15001500
Minimum of Cross-correlation0.14622450.1345435
NSC (Normalized Strand Cross-correlation coeff.)1.0269641.026393
RSC (Relative Strand Cross-correlation coeff.)0.090925930.05393409


Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.


rep1
rep1
rep2
rep2

Jensen-Shannon distance (filtered/deduped BAM)

rep1rep2
AUC0.273934742705974570.26180547357387196
Synthetic AUC0.493299004023565630.4928093461905972
X-intercept0.112777789998460190.12441032429913831
Synthetic X-intercept1.1671355817523142e-1902.267792405421769e-165
Elbow Point0.60054033191817830.6059556495881518
Synthetic Elbow Point0.50441960062785130.5122545607765389
JS Distance0.15001564108809160.17123229799460005
Synthetic JS Distance0.292116651887430130.3080898776864552
% Genome Enriched28.62339345242499530.280784621137737
Diff. Enrichment23.20286747355447725.44326296243884
CHANCE Divergence0.198390504515148750.2172965290937639

Peak enrichment


Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

rep1rep2rep1-pr1rep2-pr1rep1-pr2rep2-pr2pooledpooled-pr1pooled-pr2
Fraction of Reads in Peaks0.20323813260068410.208044801851825080.219665193148138840.22612244492376290.219741827908867150.226131748530679850.198427644484167330.203452924687090970.2035529242669246

FRiP for overlap peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.117641559529632150.105682331934404070.104795291105949510.11822428108805347

FRiP for IDR peaks

rep1_vs_rep2rep1-pr1_vs_rep1-pr2rep2-pr1_vs_rep2-pr2pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks0.070409126558348010.0581861551098973860.0618691289250540640.06925813642709379

For spp raw peaks:


For overlap/IDR peaks: